After you use the Add Appliction/File/Folder/Website buttons to add them to the list in the Shortcuts window, make sure to click the Save button to have them applied to the taskbar. Note that Application shortcuts will also combine with running programs by default.

Another way you can add Application shortcuts is by moving the program to the second monitor, then right-click the taskbar button and choose "Pin to Taskbar."

If you still run into any trouble, could you email a screenshot of the Taskbar Shortcuts window and the taskbar itself to us at support@displayfusion.com?

I figured it out. I was trying to add the Shortcuts to my default monitor without the other one hooked up. Now that I have both monitors, I see that it adds it only to the secondary monitor. Is there any way I can add Folders and Files to the taskbar on my primary with DF? I see that the taskbar options all work for the "DisplayFusion taskbar", but can I do all the same things to the default one, like move the taskbar to the top and whatnot?